The Sorghum bicolor Root Exudate Sorgoleone Shapes Bacterial Communities and Delays Network Formation

Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders in Acinetobacter pittii

Interactions between plants and soil microbial communities that benefit plant growth and enhance nutrient acquisition are driven by the selective release of metabolites from plant roots, or root exudation. To investigate these plant-microbe interactions, we developed a photoaffinity probe based on sorgoleone (sorgoleone diazirine alkyne for photoaffinity labeling, SoDA-PAL), a hydrophobic secondary metabolite and allelochemical produced in Sorghum bicolor root exudates. We applied SoDA-PAL to the identification of sorgoleone-binding proteins in Acinetobacter pittii SO1, a potential plant growth-promoting microbe isolated from sorghum rhizosphere soil. Competitive photoaffinity labeling of A. pittii whole cell lysates with SoDA-PAL identified 137 statistically enriched proteins, including putative transporters, transcriptional regulators, and a subset of proteins with predicted enzymatic functions. We performed computational protein modeling and docking with sorgoleone to prioritize candidates for experimental validation and then confirmed binding of sorgoleone to four of these proteins in vitro: the α/β fold hydrolase SrgB (OH685_09420), a fumarylacetoacetase (OH685_02300), a lysophospholipase (OH685_14215), and an unannotated hypothetical protein (OH685_18625). Our application of this specialized sorgoleone-based probe coupled with structural bioinformatics streamlines the identification of microbial proteins involved in metabolite recognition, metabolism, and toxicity, widening our understanding of the range of cellular pathways that can be affected by a plant secondary metabolite.IMPORTANCEHere, we demonstrate that a photoaffinity-based chemical probe modeled after sorgoleone, an important secondary metabolite released by sorghum roots, can be used to identify microbial proteins that directly interact with sorgoleone. We applied this probe to the sorghum-associated bacterium Acinetobacter pittii and showed that probe labeling is dose-dependent and sensitive to competition with purified sorgoleone. Coupling the probe with proteomics and computational analysis facilitated the identification of putative sorgoleone binders, including a protein implicated in a conserved pathway essential for sorgoleone catabolism. We anticipate that discoveries seeded by this workflow will expand our understanding of the molecular mechanisms by which specific metabolites in root exudates shape the sorghum rhizosphere microbiome.

Engineering agricultural soil microbiomes and predicting plant phenotypes

Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use efficiency, plant tolerance to stressors, and confer benefits to future generations of crops grown in the same soil. Unlocking the potential of microbial communities in the rhizosphere and endosphere is therefore of great interest for sustainable agriculture advancements. Before plant microbiomes can be engineered to confer desirable phenotypic effects on their plant hosts, a deeper understanding of the interacting factors influencing rhizosphere community structure and function is needed. Dealing with this complexity is becoming more feasible using computational approaches. In this review, we discuss recent advances at the intersection of experimental and computational strategies for the investigation of plant-microbiome interactions and the engineering of desirable soil microbiomes.

Roots of synthetic ecology: microbes that foster plant resilience in the changing climate

Microbes orchestrate nearly all major biogeochemical processes. The ability to program their influence on plant growth and development is attractive for sustainable agriculture. However, the complexity of microbial ecosystems and our limited understanding of the mechanisms by which plants and microbes interact with each other and the environment make it challenging to use microbiomes to influence plant growth. Novel technologies at the intersection of microbial ecology, systems biology, and bioengineering provide new tools to probe the role of plant microbiomes across environments. Here, we summarize recent studies on plant and microbe responses to abiotic stresses, showcasing key molecules and micro-organisms that are important for plant health. We highlight opportunities to use synthetic microbial communities to understand the complexity of plant-microbial interactions and discuss future avenues of programming ecology to improve plant and ecosystem health.

Enhancing agroecosystem nitrogen management: microbial insights for improved nitrification inhibition

Nitrification is a key microbial process in the nitrogen (N) cycle that converts ammonia to nitrate. Excessive nitrification, typically occurring in agroecosystems, has negative environmental impacts, including eutrophication and greenhouse gas emissions. Nitrification inhibitors (NIs) are widely used to manage N in agricultural systems by reducing nitrification rates and improving N use efficiency. However, the effectiveness of NIs can vary depending on the soil conditions, which, in turn, affect the microbial community and the balance between different functional groups of nitrifying microorganisms. Understanding the mechanisms underlying the effectiveness of NIs, and how this is affected by the soil microbial communities or abiotic factors, is crucial for promoting sustainable fertilizer practices. Therefore, this review examines the different types of NIs and how abiotic parameters can influence the nitrifying community, and, therefore, the efficacy of NIs. By discussing the latest research in this field, we provide insights that could facilitate the development of more targeted, efficient, or complementary NIs that improve the application of NIs for sustainable management practices in agroecosystems.

C4 cereal and biofuel crop microbiomes

Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.

Nitrogen-loss and carbon-footprint reduction by plant-rhizosphere exudates

Low-carbon approaches to agriculture constitute a pivotal measure to address the challenge of global climate change. In agroecosystems, rhizosphere exudates are significantly involved in regulating the nitrogen (N) cycle and facilitating belowground chemical communication between plants and soil microbes to reduce direct and indirect emissions of greenhouse gases (GHGs) and control N runoff from cultivated sites into natural water bodies. Here, we discuss specific rhizosphere exudates from plants and microorganisms and the mechanisms by which they reduce N loss and subsequent N pollution in terrestrial and aquatic environments, including biological nitrification inhibitors (BNIs), biological denitrification inhibitors (BDIs), and biological denitrification promoters (BDPs). We also highlight promising application scenarios and challenges in relation to rhizosphere exudates in terrestrial and aquatic environments.

High Frankia abundance and low diversity of microbial community are associated with nodulation specificity and stability of sea buckthorn root nodule

Introduction

Actinorhizal symbioses are gaining attention due to the importance of symbiotic nitrogen fixation in sustainable agriculture. Sea buckthorn (Hippophae L.) is an important actinorhizal plant, yet research on the microbial community and nitrogen cycling in its nodules is limited. In addition, the influence of environmental differences on the microbial community of sea buckthorn nodules and whether there is a single nitrogen-fixing actinomycete species in the nodules are still unknown.

Methods

We investigated the diversity, community composition, network associations and nitrogen cycling pathways of the microbial communities in the root nodule (RN), nodule surface soil (NS), and bulk soil (BS) of Mongolian sea buckthorn distributed under three distinct ecological conditions in northern China using 16S rRNA gene and metagenomic sequencing. Combined with the data of environmental factors, the effects of environmental differences on different sample types were analyzed.

Results

The results showed that plants exerted a clear selective filtering effect on microbiota, resulting in a significant reduction in microbial community diversity and network complexity from BS to NS to RN. Proteobacteria was the most abundant phylum in the microbiomes of BS and NS. While RN was primarily dominated by Actinobacteria, with Frankia sp. EAN1pec serving as the most dominant species. Correlation analysis indicated that the host determined the microbial community composition in RN, independent of the ecological and geographical environmental changes of the sea buckthorn plantations. Nitrogen cycle pathway analyses showed that RN microbial community primarily functions in nitrogen fixation, and Frankia sp. EAN1pec was a major contributor to nitrogen fixation genes in RN.

Discussion

This study provides valuable insights into the effects of eco-geographical environment on the microbial communities of sea buckthorn RN. These findings further prove that the nodulation specificity and stability of sea buckthorn root and Frankia sp. EAN1pec may be the result of their long-term co-evolution.

Interactions between root hairs and the soil microbial community affect the growth of maize seedlings

Root hairs are considered important for rhizosphere formation, which affects root system functioning. Through interactions with soil microorganisms mediated by root exudation, root hairs may affect the phenotypes and growth of young plants. We tested this hypothesis by integrating results from two experiments: (1) a factorial greenhouse seedling experiment with Zea mays B73-wt and its root-hairless mutant, B73-rth3, grown in live and autoclaved soil, quantifying 15 phenotypic traits, seven growth rates, and soil microbiomes and (2) a semi-hydroponic system quantifying root exudation of maize genotypes. Possibly as compensation for lacking root hairs, B73-rth3 seedlings allocated more biomass to roots and grew slower than B73-wt seedlings in live soil, whereas B73-wt seedlings grew slowest in autoclaved soil, suggesting root hairs can be costly and their benefits were realized with more complete soil microbial assemblages. There were substantial differences in root exudation between genotypes and in rhizosphere versus non-rhizosphere microbiomes. The microbial taxa enriched in the presence of root hairs generally enhanced growth compared to taxa enriched in their absence. Our findings suggest the root hairs' adaptive value extends to plant-microbe interactions mediated by root exudates, affecting plant phenotypes, and ultimately, growth.

The Chemical Ecology of Plant Natural Products

Plants are excellent chemists with an impressive capability of biosynthesizing a large variety of natural products (also known as secondary or specialized metabolites) to resist various biotic and abiotic stresses. In this chapter, 989 plant natural products and their ecological functions in plant-herbivore, plant-microorganism, and plant-plant interactions are reviewed. These compounds include terpenoids, phenols, alkaloids, and other structural types. Terpenoids usually provide direct or indirect defense functions for plants, while phenolic compounds play important roles in regulating the interactions between plants and other organisms. Alkaloids are frequently toxic to herbivores and microorganisms, and can therefore also provide defense functions. The information presented should provide the basis for in-depth research of these plant natural products and their natural functions, and also for their further development and utilization.

Persistence of Root Exudates of Sorghum bicolor and Solidago canadensis: Impacts on Invasive and Native Species

Root exudates of the invasive Solidago canadensis and the cereal crop Sorghum bicolor (L.) Moench cv. 'Hybridsorgo' were tested for allelopathic interactions against native and invasive plant species in a controlled environment. After the surface was sterilized, the seeds of two invasive species (Bromus sterilis and Veronica persica) and two native species (Youngia japonica and Rumex acetosa) were germinated and transplanted into the soil (1:1 mixture of coco peat and sand) that had been conditioned for one month by the cultivation of Solidago canadensis and Sorghum bicolor, both in combination or as unplanted controls. After an additional eight weeks of growth, morphometric measurements of the shoot and root, including foliar characteristics and above- and below-ground biomass accumulation, were performed. The results revealed significant inhibitory effects of root exudates released by Sorghum bicolor and Solidago canadensis on native species' productivity and physiology. The invasive species exhibited variable growth responses, with Veronica persica showing reduced shoot and root expansion, but Bromus sterilis revealed increased shoot and root biomass allocation and nutrition under the exudate treatments. Exudates from Solidago canadensis and Sorghum bicolor together showed synergistic negative effects on native species, while they promoted growth and nutrition in Veronica persica. Taken together, the differential species responses indicate that the tested native species were more sensitive to the allelopathic compounds than the invasive species, which is in line with the theory of novel weapons. The legacy effects of root exudates of both Sorghum bicolor and Solidago canadensis could promote invasive establishment through imposing allelochemical interference competition against native plant species. Understanding the specific allelopathic mechanisms may help with the development of integrated strategies for managing invasive species.

Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome

Plants exude specialized metabolites from their roots, and these compounds are known to structure the root microbiome. However, the underlying mechanisms are poorly understood. We established a representative collection of maize root bacteria and tested their tolerance against benzoxazinoids (BXs), the dominant specialized and bioactive metabolites in the root exudates of maize plants. In vitro experiments revealed that BXs inhibited bacterial growth in a strain- and compound-dependent manner. Tolerance against these selective antimicrobial compounds depended on bacterial cell wall structure. Further, we found that native root bacteria isolated from maize tolerated the BXs better compared to nonhost Arabidopsis bacteria. This finding suggests the adaptation of the root bacteria to the specialized metabolites of their host plant. Bacterial tolerance to 6-methoxy-benzoxazolin-2-one (MBOA), the most abundant and selective antimicrobial metabolite in the maize rhizosphere, correlated significantly with the abundance of these bacteria on BX-exuding maize roots. Thus, strain-dependent tolerance to BXs largely explained the abundance pattern of bacteria on maize roots. Abundant bacteria generally tolerated MBOA, while low abundant root microbiome members were sensitive to this compound. Our findings reveal that tolerance to plant specialized metabolites is an important competence determinant for root colonization. We propose that bacterial tolerance to root-derived antimicrobial compounds is an underlying mechanism determining the structure of host-specific microbial communities.

Engineering the Crop Microbiota Through Host Genetics

The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.

Application of plant specialized metabolites to modulate soil microbiota

Plant specialized metabolites (PSMs) are considerably diverse compounds with multifaceted roles in the adaptation of plants to various abiotic and biotic stresses. PSMs are frequently secreted into the rhizosphere, a small region around the roots, where they facilitate interactions between plants and soil microorganisms. PSMs shape the host-specific rhizosphere microbial communities that potentially influence plant growth and tolerance to adverse conditions. Plant mutants defective in PSM biosynthesis contribute to reveal the roles of each PSM in plant-microbiota interactions in the rhizosphere. Recently, various approaches have been used to directly supply PSMs to soil by in vitro methods or through addition in pots with plants. This review focuses on the feasibility of the direct PSM application methods to reveal rhizospheric plant-microbiota interactions and discusses the possibility of applying the knowledge gained to future engineering of rhizospheric traits.

An optimized hydroponic pipeline for large-scale identification of wheat genotypes with resilient biological nitrification inhibition activity

Several plant species have been reported to inhibit nitrification via their root exudates, the so-called biological nitrification inhibition (BNI). Given the potential of BNI-producing plants to sustainably mitigate N losses in agrosystems, identification of BNI activity in existing germplasms is of paramount importance. A hydroponic system was combined with an optimized Nitrosomonas europaea-based bioassay to determine the BNI activity of root exudates. The pipeline allows collecting and processing hundreds of root exudates simultaneously. An additional assay was established to assess the potential bactericide effect of the root exudates. The pipeline was used to unravel the impact of developmental stage, temperature and osmotic stress on the BNI trait in selected wheat genotypes. Biological nitrification inhibition activity appeared consistently higher in wheat at the pretillering stage as compared to the tillering stage. While low-temperatures did not alter BNI activities in root exudates, osmotic stress appeared to change the BNI activity in a genotype-dependent manner. Further analysis of Nitrosomonas culture after pre-exposure to root exudates suggested that BNI activity has no or limited bactericide effects. The present pipeline will be instrumental to further investigating the dynamics of BNI activity and to uncover the diversity of the BNI trait in plant species.

Responses of sorghum to cold stress: A review focused on molecular breeding

Climate change has led to the search for strategies to acclimatize plants to various abiotic stressors to ensure the production and quality of crops of commercial interest. Sorghum is the fifth most important cereal crop, providing several uses including human food, animal feed, bioenergy, or industrial applications. The crop has an excellent adaptation potential to different types of abiotic stresses, such as drought, high salinity, and high temperatures. However, it is susceptible to low temperatures compared with other monocotyledonous species. Here, we have reviewed and discussed some of the research results and advances that focused on the physiological, metabolic, and molecular mechanisms that determine sorghum cold tolerance to improve our understanding of the nature of such trait. Questions and opportunities for a comprehensive approach to clarify sorghum cold tolerance or susceptibility are also discussed.

Syringic acid from rice roots inhibits soil nitrification and N2O emission under red and paddy soils but not a calcareous soil

Syringic acid (SA) is a novel biological nitrification inhibitor (BNIs) discovered in rice root exudates with significant inhibition of Nitrosomonas strains. However, the inhibitory effect of SA on nitrification and nitrous oxide (N₂O) emissions in different soils and the environmental factors controlling the degree of inhibition have not been studied. Using 14-day microcosm incubation, we investigated the effects of different concentrations of SA on nitrification activity, abundance of ammonia-oxidizing microorganisms, and N₂O emissions in three typical agricultural soils. The nitrification inhibitory efficacy of SA was strongest in acidic red soil, followed by weakly acidic paddy soil, with no significant effect in an alkaline calcareous soil. Potential nitrification activity (PNA) were also greatly reduced by SA additions in paddy and red soil. Pearson correlation analysis showed that the inhibitory efficacy of SA might be negatively correlated with soil pH and positively correlated with clay percentage. SA treatments significantly reduced N₂O emissions by 69.1-79.3% from paddy soil and by 40.8%-46.4% from red soil, respectively, but no effect was recorded in the calcareous soil. SA addition possessed dual inhibition of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) abundance in paddy and red soil. Structural equation modelling revealed that soil ammonium (NH₄ ⁺) and dissolved organic carbon content (DOC) were the key variables explaining AOA and AOB abundance and subsequent N₂O emissions. Our results support the potential for the use of the BNI SA in mitigating N₂O emissions and enhancing N utilization in red and paddy soils.

Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes

Root exudates are important for shaping root-associated microbiomes. However, studies on a wider range of metabolites in exudates are required for a comprehensive understanding about their influence on microbial communities. We identified maize inbred lines that differ in exudate concentrations of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and γ-aminobutyric acid (GABA) using a semi-hydroponic system. These lines were grown in the field to determine the changes in microbial diversity and gene expression due to varying concentrations of DIMBOA and GABA in exudates using 16S rRNA amplicon sequencing and metatranscriptomics. Results showed individual and interaction effects of DIMBOA and GABA on the rhizosphere and root endosphere β-diversity, most strongly at the V10 growth stage. The main bacterial families affected by both compounds were Ktedonobacteraceae and Xanthomonadaceae. Higher concentrations of DIMBOA in exudates affected the rhizosphere metatranscriptome, enriching for metabolic pathways associated with plant disease. This study validated the use of natural variation within plant species as a powerful approach for understanding the role of root exudates on microbiome selection. We also showed that a semi-hydroponic system can be used to identify maize genotypes that differ in GABA and DIMBOA exudate concentrations under field conditions. The impact of GABA exudation on root-associated microbiomes is shown for the first time.

Applications of the indole-alkaloid gramine modulate the assembly of individual members of the barley rhizosphere microbiota

Microbial communities proliferating at the root-soil interface, collectively referred to as the rhizosphere microbiota, represent an untapped beneficial resource for plant growth, development and health. Integral to a rational manipulation of the microbiota for sustainable agriculture is the identification of the molecular determinants of these communities. In plants, biosynthesis of allelochemicals is centre stage in defining inter-organismal relationships in the environment. Intriguingly, this process has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but has been counter selected in several modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how exogenous applications of gramine impacted on the rhizosphere microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. High throughput 16S rRNA gene amplicon sequencing revealed that applications of gramine interfere with the proliferation of a subset of soil microbes with a relatively broad phylogenetic assignment. Strikingly, growth of these bacteria appeared to be rescued by barley plants in a genotype- and dosage-independent manner. In parallel, we discovered that host recruitment cues can interfere with the impact of gramine application in a host genotype-dependent manner. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the prokaryotic communities inhabiting the root-soil interface.

Integration of omics data to unravel root microbiome recruitment

The plant microbiome plays an essential role in supporting plant growth and health, but plant molecular mechanisms underlying its recruitment are still unclear. Multi-omics data integration methods can be used to unravel new signalling relationships. Here, we review the effects of plant genetics and root exudates on root microbiome recruitment, and discuss methodological advances in data integration approaches that can help us to better understand and optimise the crop-microbiome interaction for a more sustainable agriculture.